Adding Settings Menu

protzilla/constants/paths.py

@@ -4,6 +4,7 @@
 USER_DATA_PATH = Path(PROJECT_PATH, "user_data")
 RUNS_PATH = USER_DATA_PATH / "runs"
 WORKFLOWS_PATH = USER_DATA_PATH / "workflows"
+SETTINGS_PATH = USER_DATA_PATH / "settings"
 EXTERNAL_DATA_PATH = Path(PROJECT_PATH, "user_data/external_data")
 WORKFLOW_META_PATH = Path(PROJECT_PATH, "protzilla/constants/workflow_meta.json")
 UI_PATH = Path(PROJECT_PATH, "ui")

protzilla/data_preprocessing/plots.py

@@ -5,9 +5,9 @@
 from plotly.graph_objects import Figure
 from plotly.subplots import make_subplots
 
+from ui.settings.plot_template import *
 from protzilla.data_preprocessing.plots_helper import generate_tics
 from protzilla.utilities import default_intensity_column
-from protzilla.utilities.plot_template import *
 from protzilla.constants.colors import *
 
 def create_pie_plot(

protzilla/utilities/utilities.py

@@ -136,3 +136,37 @@ def get_file_name_from_upload_path(upload_path: str) -> str:
     base_name = file_name_randomized.split("_")[0]
     file_extension = file_name_randomized.split(".")[-1]
     return f"{base_name}.{file_extension}"
+
+
+def parameters_from_post(post):
+    d = dict(post)
+    if "csrfmiddlewaretoken" in d:
+        del d["csrfmiddlewaretoken"]
+    parameters = {}
+    for k, v in d.items():
+        if len(v) > 1:
+            # only used for named_output parameters and multiselect fields
+            parameters[k] = v
+        else:
+            parameters[k] = convert_str_if_possible(v[0])
+    return parameters
+
+
+def convert_str_if_possible(s):
+    try:
+        f = float(s)
+        return int(f) if int(f) == f else f
+    except ValueError:
+        if s == "checked":
+            # s is a checkbox
+            return True
+        if re.fullmatch(r"\d+(\.\d+)?(\|\d+(\.\d+)?)*", s):
+            # s is a multi-numeric input e.g. 1-0.12-5
+            numbers_str = re.findall(r"\d+(?:\.\d+)?", s)
+            numbers = []
+            for num in numbers_str:
+                num = float(num)
+                num = int(num) if int(num) == num else num
+                numbers.append(num)
+            return numbers
+        return s

ui/main/settings.py

@@ -47,6 +47,7 @@
     "django.contrib.messages",
     "django.contrib.staticfiles",
     "runs",
+    "settings",
 ]
 
 MIDDLEWARE = [
@@ -127,7 +128,10 @@
 
 STATIC_URL = "static/"
 
-STATICFILES_DIRS = [BASE_DIR / "static"]
+STATICFILES_DIRS = [
+    BASE_DIR / "static",
+    BASE_DIR / "settings/static"
+    ]
 
 # Default primary key field type
 # https://docs.djangoproject.com/en/4.1/ref/settings/#default-auto-field

ui/main/urls.py

@@ -21,6 +21,7 @@
 urlpatterns = [
     path("", views.index),
     path("runs/", include("runs.urls")),
+    path("settings/", include("settings.urls")),
     path("databases", views.databases, name="databases"),
     path("databases/upload", views.database_upload, name="database_upload"),
     path("databases/delete", views.database_delete, name="database_delete"),

ui/main/views.py

@@ -19,6 +19,7 @@ def index(request):
 
 
 def databases(request):
+    request.session['last_view'] = "databases"
     databases = uniprot_databases()
     df_infos = {}
     if database_metadata_path.exists():

ui/runs/static/runs/style.css

@@ -88,4 +88,10 @@ html, body {
     padding: 10px 8%;
     margin-top: 10px;
     background-color: rgb(255, 255, 255);
+}
+.plot-wrapper {
+    width: fit-content;
+    height: fit-content;
+    border: 1px solid #e8edf3;
+    border-radius: .375rem;
 }

ui/runs/templates/runs/details.html

@@ -215,7 +215,7 @@ <h3>{{ display_name }}</h3>
                 {% if current_plots %}
                     <div class="mt-4" id="plots">
                         {% for plot in current_plots %}
-                            <div class="plot-wrapper">
+                            <div class="plot-wrapper mb-2">
                                 {{ plot|safe }}
                             </div>
                         {% endfor %}
@@ -225,15 +225,13 @@ <h3>{{ display_name }}</h3>
                     <div class="d-flex col">
                         {% if current_plots %}
                             <form action="{% url 'runs:download_plots' run_name %}">
-                                <select class="form-select mb-2" name="format">
-                                    <option value="png" selected="selected">png</option>
-                                    <option value="tiff">tiff</option>
-                                    <option value="svg">svg</option>
-                                    <option value="pdf">pdf</option>
-                                    <option value="eps">eps</option>
-                                    <option value="jpg">jpg</option>
-                                </select>
-                                <button class="btn btn-grey">Download plots</button>
+                                <button class="btn btn-grey d-flex align-items-center">
+                                    <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-download me-2" viewBox="0 0 16 16">
+                                        <path d="M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5"/>
+                                        <path d="M7.646 11.854a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V1.5a.5.5 0 0 0-1 0v8.793L5.354 8.146a.5.5 0 1 0-.708.708z"/>
+                                    </svg>
+                                    Download plots
+                                </button>
                             </form>
                         {% endif %}
                     </div>
@@ -278,11 +276,11 @@ <h5 class="modal-title" id="calculationInProgressModalLabel">Do you want back?</
                                                             Do you want to proceed?
                                                             <hr>
                                                             <a href="{% url 'runs:back' run_name %}" id = "backButton" class="btn btn-red mr-auto">Back</a>
-                                                            <button id= "cancel" type="button" class="btn btn-secondary" data-dismiss="modal">Cancel</button>
+                                                            <button id="cancel" type="button" class="btn btn-secondary" data-dismiss="modal">Cancel</button>
+                                                        </div>
                                                     </div>
                                                 </div>
                                             </div>
-                                        </div>
                                         {% endif %}
                                         {% if not last_step %}
                                           <button class="btn btn-red" {% if not results_exist %} disabled {% endif %} >Next</button>

ui/runs/views.py

@@ -29,6 +29,7 @@
     format_trace,
     get_memory_usage,
     name_to_title,
+    parameters_from_post,
 )
 from protzilla.workflow import get_available_workflow_names
 from protzilla.constants.paths import WORKFLOWS_PATH
@@ -38,13 +39,14 @@
     make_name_field,
     make_sidebar,
 )
-from ui.runs.views_helper import display_message, display_messages, parameters_from_post
+from ui.runs.views_helper import display_message, display_messages
 
 from .form_mapping import (
     get_empty_plot_form_by_method,
     get_filled_form_by_method,
     get_filled_form_by_request,
 )
+from ui.settings.views import get_settings
 
 active_runs: dict[str, Run] = {}
 
@@ -68,6 +70,9 @@ def detail(request: HttpRequest, run_name: str):
         active_runs[run_name] = Run(run_name)
     run: Run = active_runs[run_name]
 
+    request.session['last_view'] = "runs:detail"
+    request.session['run_name'] = run_name
+
     # section, step, method = run.current_run_location()
     # end_of_run = not step
 
@@ -173,6 +178,9 @@ def index(request: HttpRequest, index_error: bool = False):
     :return: the rendered index page
     :rtype: HttpResponse
     """
+
+    request.session['last_view'] = "runs:index"
+
     return render(
         request,
         "runs/index.html",
@@ -447,7 +455,8 @@ def download_plots(request: HttpRequest, run_name: str):
     if run_name not in active_runs:
         active_runs[run_name] = Run(run_name)
     run = active_runs[run_name]
-    format_ = request.GET["format"]
+    settings = get_settings("plots")
+    format_ = settings["file_format"]
     index = run.steps.current_step_index
     section = run.current_step.section
     operation = run.current_step.operation

ui/runs/views_helper.py

@@ -8,40 +8,6 @@
 from ui.runs.utilities.alert import build_trace_alert
 
 
-def parameters_from_post(post):
-    d = dict(post)
-    if "csrfmiddlewaretoken" in d:
-        del d["csrfmiddlewaretoken"]
-    parameters = {}
-    for k, v in d.items():
-        if len(v) > 1:
-            # only used for named_output parameters and multiselect fields
-            parameters[k] = v
-        else:
-            parameters[k] = convert_str_if_possible(v[0])
-    return parameters
-
-
-def convert_str_if_possible(s):
-    try:
-        f = float(s)
-        return int(f) if int(f) == f else f
-    except ValueError:
-        if s == "checked":
-            # s is a checkbox
-            return True
-        if re.fullmatch(r"\d+(\.\d+)?(\|\d+(\.\d+)?)*", s):
-            # s is a multi-numeric input e.g. 1-0.12-5
-            numbers_str = re.findall(r"\d+(?:\.\d+)?", s)
-            numbers = []
-            for num in numbers_str:
-                num = float(num)
-                num = int(num) if int(num) == num else num
-                numbers.append(num)
-            return numbers
-        return s
-
-
 def get_displayed_steps(
     steps: StepManager,
 ) -> list[dict]:  # TODO i think this broke with the new naming scheme, should be redone

ui/settings/apps.py

@@ -0,0 +1,6 @@
+from django.apps import AppConfig
+
+
+class SettingsV2Config(AppConfig):
+    default_auto_field = "django.db.models.BigAutoField"
+    name = "settings"

ui/settings/plot_template.py

@@ -0,0 +1,78 @@
+import plotly.io as pio
+import plotly.graph_objects as go
+
+from protzilla.disk_operator import YamlOperator
+from protzilla.constants.colors import PLOT_PRIMARY_COLOR, PLOT_SECONDARY_COLOR
+from protzilla.constants.paths import SETTINGS_PATH
+
+def get_settings(section_id: str):
+    op = YamlOperator()
+    path = SETTINGS_PATH / (section_id + ".yaml")
+    settings = op.read(path)
+    return settings
+
+def determine_font(params: dict):
+    """
+    This method determines if a custom font was selected or not.
+    """
+    if(params["font"] == "Custom"):
+        font = params["custom_font"]
+    else:
+        font = params["font"]
+    return font
+
+class PlotTemplate:
+    def __init__(self):
+        params = get_settings("plots")
+        font = determine_font(params)
+        self.layout = go.Layout(
+            title={
+                "font": {
+                    "size": params["heading_size"],
+                    "family": font
+                },
+                "y": 0.98,
+                "x": 0.5,
+                "xanchor": "center",
+                "yanchor": "top"
+            },
+            font={
+                "size": params["text_size"],
+                "family": font
+            },
+            colorway=[PLOT_PRIMARY_COLOR, PLOT_SECONDARY_COLOR],
+            plot_bgcolor="white",
+            yaxis={
+                "gridcolor": "lightgrey",
+                "zerolinecolor": "lightgrey"
+            },
+            modebar={
+                "remove": ["autoScale2d", "lasso", "lasso2d", "toImage", "select2d"],
+            },
+            dragmode="pan",
+            height=params["height"],
+            width=params["width"]
+        )
+
+    def update(self, params: dict):
+        """
+        Updates the used Plotly template. If the dictionary contains a known key, the value will be accepted and saved.
+        :param params: Dictionary containing properties of the Plotly template.
+        """
+        font = determine_font(params)
+        self.layout.title.font.size = params["heading_size"]
+        self.layout.title.font.family = font
+        self.layout.font.size = params["text_size"]
+        self.layout.font.family = font
+        self.layout.height = params["height"]
+        self.layout.width = params["width"]
+
+    def apply(self):
+        """
+        Applies the current template as default template.
+        """
+        pio.templates["plotly_protzilla"] = go.layout.Template(layout=self.layout)
+
+template = PlotTemplate()
+template.apply()
+pio.templates.default = "plotly_protzilla"

ui/settings/static/settings.js

@@ -0,0 +1,15 @@
+$( document ).ready(function () {
+    $("#customFontInput").click(function () {
+        const radio = document.getElementById('customFontRadio');
+        const input = document.getElementById('customFontInput');
+        radio.checked = true;
+    })
+
+    $(".action-button").each(function () {
+        $(this).click(function () {
+            const form = document.getElementById("settings-form");
+            form.action = $(this).data("action");
+            form.submit();
+        });
+    });
+});